3EI1 Dna Binding Protein Dna date Sep 15, 2008
title Structure Of Hsddb1-Drddb2 Bound To A 14 Bp 6-4 Photoproduct Containing Dna-Duplex
authors A.Scrima, N.H.Thoma
compound source
Molecule: Dna Damage-Binding Protein 1
Chain: A
Synonym: Hsddb1, Damage-Specific Dna-Binding Protein 1, Uv- Damaged Dna-Binding Factor, Ddb P127 Subunit, Dna Damage- Binding Protein A, Ddba, Uv-Damaged Dna-Binding Protein 1, Uv-Ddb 1, Xeroderma Pigmentosum Group E-Complementing Protein, Xpce, Xpe-Binding Factor, Xpe-Bf, Hbv X- Associated Protein 1, Xap-1;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ddb1, Xap1
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111
Expression_system_cell_line: Bti-Tn-5b1-4
Expression_system_cell: High Five Cells
Expression_system_vector_type: Baculovirus
Expression_system_vector: Pac-Derived

Molecule: Dna Damage-Binding Protein 2
Chain: B
Synonym: Damage-Specific Dna-Binding Protein 2
Engineered: Yes

Organism_scientific: Danio Rerio
Organism_common: Zebrafish
Organism_taxid: 7955
Gene: Ddb2, Si:Dkey-45f10.3
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111
Expression_system_cell_line: Bti-Tn-5b1-4
Expression_system_cell: High Five Cells
Expression_system_vector_type: Baculovirus
Expression_system_vector: Pac-Derived

Molecule: 5'-D(Dapdcpdgpdcpdgpdap(64t)P(5py) Pdgpdcpdgpdcpdcpdc)-3';
Chain: G
Engineered: Yes

Synthetic: Yes

Molecule: 5'- D(Dtpdgpdgpdgpdcpdgpdcpdapdapdtpdcpdgpdcpdg)- 3';
Chain: H
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 21 21 21
R_factor 0.220 R_Free 0.278
crystal
cell
length a length b length c angle alpha angle beta angle gamma
112.740 123.600 158.370 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand 5PY, 64T, PG4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


B


Primary referenceStructural basis of UV DNA-damage recognition by the DDB1-DDB2 complex., Scrima A, Konickova R, Czyzewski BK, Kawasaki Y, Jeffrey PD, Groisman R, Nakatani Y, Iwai S, Pavletich NP, Thoma NH, Cell. 2008 Dec 26;135(7):1213-23. PMID:19109893
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (253 Kb) [Save to disk]
  • Biological Unit Coordinates (3ei1.pdb1.gz) 246 Kb
  • LPC: Ligand-Protein Contacts for 3EI1
  • CSU: Contacts of Structural Units for 3EI1
  • Likely Quarternary Molecular Structure file(s) for 3EI1
  • Structure Factors (834 Kb)
  • Retrieve 3EI1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3EI1 from S2C, [Save to disk]
  • Re-refined 3ei1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3EI1 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 3EI1
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3EI1, from MSDmotif at EBI
  • Fold representative 3ei1 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3ei1_H] [3ei1_G] [3ei1_B] [3ei1_A] [3ei1]
  • SWISS-PROT database: [Q16531] [Q2YDS1]
  • Domain organization of [DDB1_HUMAN] [DDB2_DANRE] by SWISSPFAM
  • Domain found in 3EI1: [WD40 ] by SMART
  • Other resources with information on 3EI1
  • Community annotation for 3EI1 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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